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Crystal structure of a putative aminoglycoside phosphotransferase (reut_a1007) from ralstonia eutropha jmp134 at 2.32 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.17 293 20.0% polyethylene glycol 8000, 0.3M calcium acetate, 0.1M MES pH 6.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.088 α = 90 b = 127.522 β = 90 c = 51.509 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-06-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97971,0.97956 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.32 28.989 99.9 0.129 0.129 5.3 3.5 18395 33.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.32 2.38 100 0.718 0.718 1.1 3.5 1329
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.32 28.989 17366 898 94.49 0.238 0.235 0.2412 0.287 0.2894 RANDOM 37.949
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -3.58 -3.53 7.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.02 r_dihedral_angle_3_deg 12.922 r_dihedral_angle_4_deg 12.686 r_scangle_it 5.791 r_scbond_it 4.271 r_dihedral_angle_1_deg 2.946 r_mcangle_it 2.776 r_mcbond_it 1.72 r_angle_refined_deg 1.479 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.02 r_dihedral_angle_3_deg 12.922 r_dihedral_angle_4_deg 12.686 r_scangle_it 5.791 r_scbond_it 4.271 r_dihedral_angle_1_deg 2.946 r_mcangle_it 2.776 r_mcbond_it 1.72 r_angle_refined_deg 1.479 r_angle_other_deg 0.939 r_mcbond_other 0.277 r_nbd_refined 0.201 r_nbd_other 0.193 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_other 0.166 r_metal_ion_refined 0.165 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.091 r_nbtor_other 0.087 r_symmetry_hbond_refined 0.039 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2563 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing